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GoParameter format

When running a Go simulation, the atoms are partitioned into chains according to the occupancy value given in the GoCoordinates file. For every possible pairwise combination between chains, a Go potential is defined by the following equations:

Let $ r^{ref}_{i,j}$ be the pairwise distance between atoms i and j in the reference structure. If $ r^{ref}_{i,j}$ is less than the Go cutoff distance, the pairwise potential between atoms i and j is given by:

$\displaystyle V_{Go}(r_{i,j},\epsilon,\sigma^{ref}_{i,j},a,b)
= 4 \epsilon \Big...
...r_{i,j}} \Bigr)^a
- \Bigl( \frac{\sigma^{ref}_{i,j}} {r_{i,j}} \Bigr)^b \Biggr]$



where $ \sigma^{ref}_{i,j}$ is given as $ \left(\frac{b}{a}\right)^{\frac{1}{b-a}}r^{ref}_{i,j}$. If $ r^{ref}_{i,j}$ is greater than the Go cutoff distance, the pairwise potential between atoms i and j is given by:

$\displaystyle V_{Go}(r_{i,j},\epsilon^{rep},\sigma^{rep},expRep) = 4 \epsilon^{rep} (\frac{\sigma^{rep}_{i,j}}{r_{i,j}})^{expRep}$

For each pairwise chain combination, the following parameters are needed to define the Go potential:

Each pairwise chaintype should be written in its own block of text with each entry given its own line. It is recommended that individual pairwise potential be separated by a blank line.


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Next: Runtime Analysis Up: Hybrid MD-Go Simulation Previous: Configuration file modifications   Contents   Index
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